This proposal seeks funding for the purchase of a first generation, ultra high performance Thermo Finnigan LTQ/FTICR MS. It is a truly exciting time for mass spectrometry, with exploding opportunities for deciphering the functional machinery of human and other cells, being enabled by dramatic new technological advances including the instrumentation proposed here. This shared instrument will be used for attomole level identification of mixtures of bio-macromolecules per se; but to a major extent for very detailed structural studies of the posttranslational and covalent status of the physiologically active forms of proteins, both intact and as their components obtained from specific enzymic and/or chemical degradation. The primary focus is on elucidation of their myriad of covalent modifications of critical importance in gaining an understanding of cell function and dysfunction through structural studies of signaling cascades, cellular communication networks, assembly and disassembly of protein machines (transcription of chromatin, etc) and cancer. This instrument will be housed in the NIH NCRR-supported Mass Spectrometry Resource at UCSF. This environment assures the availability and involvement of the scientific, technical and management expertise required to optimize its performance and research productivity. The primary theme of the major users focuses on defining the posttranslational status (including patterns of modifications) of proteins as well as their temporal processing and covalent structural modulation. They are a group of 6 Principal Investigators involved in some 21 NIH supported research programs. These investigators have established needs for better technology to address phosphorylation, O-GIcNAcylation, sulfonation, acetylation, methylation and other posttranslational and chemical modifications that will be studied with the proposed instrumentation. These research projects are at the forefront of biomedical problems deciphering natural and aberrant proteins involved in cell function and dysfunction, respectively. Most of these studies require enhanced sensitivity, electron capture dissociation, 'top down' mass balance and fast recording of CID spectra during capillary HPLC component elution times. Dr. Shokat will chair the Advisory Committee responsible for overall guidance of the shared instrument's use. Mr. David Maltby will oversee optimization of performance, scheduling, training and maintenance and will provide daily supervision of usage. Long term productive usage will be assured by the close association with the UCSF - NCRR Resource and financial support of the major users.